Okay, we've reverted to the old format for log downloads, restoring the single column (Column Z) that had been removed, with our apologies for the disruption and inconvenience. However, in cases where that column does not contain any data, the column header label now will also be omitted, so the column will still be present in the file but otherwise unpopulated with any data.
Hopefully, this still should prevent most of the previous, considerable confusion among merchants who didn't realize there were two places in the log where affiliate shares could be reported (and the most obvious of which was always blank as of the past year-plus). For this reason, we are also still omitting the obsolete column from the online display of Transaction Log views in a browser.
@mkp007: Current log downloads show the shipping total reported only once per order, logged with the first item in multi-item orders. I'm not sure what was happening before, but it appears to be fine now that Development has reverted to the old download format.